The role of the Holder lab in the Open Tree of Life effort

The primary research goal of the students, postdoctoral researchers, and Mark Holder in this effort will be to develop and improve methods for automatically updating gene tree estimates when new sequence data becomes available. This will entail automated alignment, alignment filtering, phylogenetic placement of the new sequences, determination of the "side effects" of the new data on the rest of the tree, and the reporting branch support for the updated tree. These gene trees will provide constantly available estimates of genealogies for several loci, and the estimates will feed into supertree estimation procedures developed by others in the Open Tree of Life project (for instance, Gordon Burleigh and Tiffani Williams).

In the first year of the project, the postdocs will contribute to the development of the TreeShare software that will provide web services for synthesizing and serving tree estimates (the development of that software will be led by Rick Ree's lab). The Holder lab will also be working on wrappers around distributed version control system (e.g. git) that can interact with the Open Tree of Life web services. These tools will allow members of collaborative teams to share data and the results of analyses while preserving a rich provenance of the analyses that were done. When the results are ready for publications, the tools will help researchers export their resulting trees to a publicly-viewable instance of TreeShare software and also help them archive their data in the relevant archival repository (e.g. TreeBase or Dryad).